When a low activity of acid α-glucosidase (GAA) is found, particularly in newborn screening programs, to differentiate α-glucosidase pseudo deficiency from true Pompe disease is important and urgent, as the result generates parental stress and also because this differentiation drives decisions related to the management of the case. Here, we report a case of GAA pseudo deficiency detected in a newborn screening performed by a private laboratory in Brazil. The confirmatory laboratory investigation performed at our service showed reduction of GAA activity on the dried blood spot, with inconclusive results when GAA activity was assayed in leukocytes. Genotyping of the GAA gene with nextgeneration sequencing revealed the common pathogenic mutation c.-32-13T>G and the "pseudo deficiency allele" p. [Gly576Ser; Glu689Lys], each one in heterozygous state and in trans. This report illustrates the need of newborn screening programs to have the adequate support to perform a comprehensive investigation whenever an abnormality is found in the initial screening test.